Mod Organizer Fallout FOMM

There are a lot of questions about MO with the fallout series of games and the use of Fallout Mod Manager with MO. I hope this post will shed some light on this subject.
Yes you can use MO to manage mods in the fallout series of games. There are a couple of caveats though.
The first caveat is that MO has mod isolation and mods that need to see other mods that are installed will not see them. The second caveat is a lot of the mods for Fallout use the fomod format for install and will not install under MO. Some reasons are that the mods are not packaged properly and some have poorly written scripts which will terminate abruptly.
These issues can be mitigated by using Fallout Mod Manager, FOMM, as an executable from inside of MO.
Download the FOMM installer from its page on the New Vegas Nexus and follow the instructions in the install wizard.
After it is installed in Windows, start MO and add it to the executables from the “Pick a program to run” drop down to the left of the Run button. Select the “Edit option to open the “Modify Executables” dialog.
In the “Modify Dialog” window, give the executable a name by clicking in the title box. Next click the button with the three dots in the “Binary” section and navigate to where you installed FOMM. In that directory click on fomm.exe and click open / OK. This will bring you back to the modify executables dialog. In that window click the Add button and then click OK.
Next you want to run FOMM for the first time. Select FOMM from the drop down to select it and press the Run button to start FOMM. Select the game to manage in the game selection window. I will use Fallout New Vegas as an example.
In the Fallout New Vegas setup window you will have two options, one is the location of the mod directory and the other is for the Install info. I suggest you change these as they will interfere with the Nexus Mod Manager if you ever wish to use that at a later time. You can set them to any folder that you like. I use a folder on my HDD that is called FOMM storage with two directories inside of that called Install info and Mods. When you are set click the Finish button.
FOMM may pop up a dialog telling you that “Fallout.ini” is read only. Tell it to make it not read only and to remember your selection. FOMM will now open the main window.
In the main window click on the Settings button to open the settings option. In the general tab remove all checks from the different options. None of that is needed. Go to the Fallout New Vegas tab and make sure the directories you set up earlier are correct. Click Ok when done.
Back in the main window you should see FalloutNV.esm and any DLC files and mods that you have installed. FOMM is working properly.
You are now ready to install those problem mods. Click on the package manager button to start the process. You will get a few popups before the package manager opens, I just select No to the questions.
Before you begin installing mods through FOMM, I would start with a clean overwrite folder and install mods in MO first when possible. If the mod will not install because of a scripting error or being improperly formatted, then use FOMM. If the mod does not rely on Unified HUD or need to see any other mod you can package it up as a mod with the “Create mod” option in MO, this will clean out the overwrite folder, or go to the overwrite directory in Windows explorer and zip it up and install it by the “Install mod from archive” button. You will have to delete the files afterwards.
Some additional thoughts to keep in mind. Install all mods in MO when you can. This will give you the most flexible option for mod conflicts in the left pane. Remember the vanilla data folder is overwritten by the MO virtual data folder and the overwrite folder always overwrites both of them.
Save all mods that rely on Unified HUD until last and install them with FOMM. These mods will be written to the overwrite folder in one big mod, which will allow Unified HUD to see the Hud menu xml files.
There is a growing debate as to leaving files in the overwrite folder or not. In this case I would leave them there. If I remember correctly FOMM throws a fit if they are moved out of the overwrite folder the next time it is run after the files are moved. This will prevent you from deactivating or removing any mods from the package manager. You have to either move them all back or hunt down the configuration flies and delete them to start all over.
i hope this helps.

Curious how FOMM can throw a fit. FOMM just gets presented the virtual filing system (VFS) which includes the overwrite directory. If you move things back in the exposed VFS they should still be on the same place. Looks as if somehow the VFS isn't completely transparent to FOMM.

Curious how FOMM can throw a fit. FOMM just gets presented the virtual filing system (VFS) which includes the overwrite directory. If you move things back in the exposed VFS they should still be on the same place. Looks as if somehow the VFS isn't completely transparent to FOMM.

That is only if they are not moved back. I have not modded FNV in a while so I was going by memory. I just reinstalled most of my Steam games as I was running out of space on the SSD so I will get to try this when I get back to FNV.

I've also tried using Sir Garnon's ( the Skyrim Performance Monitor dude) new Archive Invalidation program, which generates the entire ArchiveInvalidation.txt instead of the BSA. I've always had a few issues with red exclamations and using the esp-less version of WFO. The program will not see the VFS and only generates a list from the actual data folder.
I tried submitting a ticket for it and I couldn't get the site to work, so not sure how to get it to work, but I like the idea of using a txt file generator so nothing is missed.

I've also tried using Sir Garnon's ( the Skyrim Performance Monitor dude) new Archive Invalidation program, which generates the entire ArchiveInvalidation.txt instead of the BSA. I've always had a few issues with red exclamations and using the esp-less version of WFO. The program will not see the VFS and only generates a list from the actual data folder.

I tried submitting a ticket for it and I couldn't get the site to work, so not sure how to get it to work, but I like the idea of using a txt file generator so nothing is missed.

I coudn't get it to work in the first place either. Didn't want to create a new account and wanted to use my gmail account. I clicked on 'login' and selected google . Now bug genie asked me to login with my gmail account. I entered username/password. Afterwards you see your bug genie profile information. Now go to the top left corner and 'the bug genie'. Now I was in the bug genie AND could create ticket. If you want to see more then initial posting you also have to be logged in. I suppose this works also for Yahoo/OpenId/etc account. Hope this also works for you.